Computational Protein Design Scientist

Encodia is a rapidly growing platform company that is developing a new generation of protein analysis tools based on single-molecule protein sequencing. Our goal is to make protein sequencing easy and ubiquitous by using a novel reverse-translation technology that turns peptide sequences into DNA. The DNA can be read by a DNA sequencer, providing a path to breakthrough proteomics research at a scale that is not practical or cost-effective using current technologies.

Job Summary

Encodia is seeking to recruit a scientist to apply machine learning, cheminformatics and structural modeling methods to build predictive models of protein binding interactions. The role will include developing computational methods to leverage large datasets; leveraging sequence and structure data in protein design; building automated end-to-end workflows for experimental design and data processing of complex datasets; and working closely with experimental biologists. This role may be performed via remote work.

Responsibilities

• Building models applying statistical and machine learning techniques to predict protein-ligand interactions.
• Designing, implementing, and maintaining novel modeling pipelines for leveraging large datasets.
• Designing high-throughput experimental screens of computationally designed proteins and ligands.
• Conducting high-throughput virtual screening utilizing modern computational techniques such as quantitative structure activity relationship models.
• Collaborating across functions to identify opportunities for machine learning, regression, and biophysical modeling.

Requirements

• PhD or equivalent experience in Computational Biology, Computational Chemistry, Computer Science, Bioinformatics, or a related field.
• Strong competency programming in Python as well as knowledge of a strongly typed language (e.g., C/C++/Java).
• Experience analyzing large scale data.
• Experience building machine learning models to associate protein or chemical structure with function.
• Strong understanding of statistical analysis and familiarity with machine learning.
• Experience with biophysical modeling for protein and enzyme design (e.g. Rosetta, anisotropic network models).
• Self-motivated with the ability to work with and support multiple groups across the organization.
• Experience with command line Linux environments.
• Knowledge of git or other version control systems.

Benefits

Encodia is an Equal Opportunity Employer. We offer a competitive and comprehensive employee benefits package including medical plans, dental insurance, vision plans, LTD, paid vacation, and a stock plan.

We do not discriminate in recruitment, hiring, training, promotion or other employment practices for reasons of race, color, religion, gender, national origin, age, sexual orientation, gender identity or expression, marital or veteran status, disability, or any other legally protected status. We are committed to building diverse teams, and we strive to create an inclusive workplace that cultivates bold innovation through collaboration and empowers our people to unleash their full potential.

Encodia requires all employees to be fully vaccinated against COVID-19 before their start date. We will reasonably accommodate employees who cannot get vaccinated because of medical reasons or sincerely-held religious beliefs to the extent that any such accommodation does not pose an undue hardship for the company.